To date, the genetic analysis of extinct archaic hominins has required the isolation and sequencing of ancient DNA obtained from fossilized remains, which is technologically challenging and limited by the number of available specimens. However, the recent discovery that gene flow occurred between archaic groups, such as Neanderthals and Denisovans, and anatomically modern humans suggests a fossil free approach for the sequencing of archaic genomes. To this end, the goals of the proposed project are to develop an innovative new paradigm for the genetic analysis of archaic human ancestors, whose DNA lives on in the genomes of modern humans. In Aim 1, we will develop novel and computationally efficient methods for identifying introgressed DNA sequences. These methods will not depend on the availability of an archaic reference sequence and will therefore facilitate the discovery of previously unknown archaic hominins, if such groups exchanged genes with modern humans. We will rigorously evaluate the power and false discovery rates of newly developed statistics through extensive coalescent simulations under a wide variety of demographic models and admixture scenarios. In Aim 2, we will leverage our access to several large-scale sequencing projects and apply these novel methods to whole-genome and exome sequences collected in over 11,000 geographically diverse individuals. We will also develop methods to comprehensively analyze the population genetics characteristics of the reconstructed archaic metagenomes and to test hypotheses such as the fitness effects of hybridization, sex-biased patterns of gene flow, and whether introgressed sequences have been subject to positive selection. The successful completion of the proposed project will extend our understanding of admixture events between archaic and modern humans, provide insight into how introgression has shaped extant patterns of human genomic diversity, and may facilitate the molecular discovery and characterization of previously unknown archaic groups that have contributed to the modern gene pool. Overall, we anticipate that fossil free sequencing of archaic genomes will be a significant advancement for the burgeoning field of paleogenomics, allowing genetic analyses that have heretofore not been possible.